Sente is a commercial application that helps academic researchers build, maintain and use their own personal collection of academic literature in their field. Sente helps users collect references from hundreds of data sources around the world, from PubMed and Thomson Web of Knowledge, to university library catalogs. Sente includes sophisticated organizational tools to help users deal with collections of thousands of references, and it is able to produce properly formatted bibliographies in any of hundreds of different formats. Sente automatically synchronizes personal libraries across all of a user’s Macs, iPads and iPhones, and Sente lets users share their libraries with any number of other people, each of whom can also access the data on their Macs and iOS devices. Sente is in use by researchers in all fields of study at all major research institutions around the world.

Navigator is the instrument control and data analysis program used with Transgenomic’s WAVE system for DNA sample analysis by DHPLC (denaturing high performance liquid chromatography). The software supports all aspects of working with the WAVE system, including: PCR amplicon design; instrument configuration, control and monitoring; and chromatographic trace analysis. This system is in use in biomedical laboratories around the world and has proven particularly useful for identifying new genetic mutations and in characterizing mixed DNA samples.

The TSC Natural History Database (TSCDB) is a web-based tool developed for the Tuberous Sclerosis Alliance for use in clinics around the country that see patients diagnosed with Tuberous Sclerosis Complex. Because of the nature of this rare genetic condition, symptoms vary widely from one person to another and they can be manifested differently over the course of many years. TSCDB was developed to track these patients over the course of their lives, including all symptoms, diagnoses, treatments and outcomes. The nature of TSC made it important that the staff on the project be able to make extensive changes to the system without actual programming changes; e.g., they can readily extend the system to support new conditions and clinical observations through the admin interface. The TSCDB has provided researchers with a wealth of information and has been invaluable in identifying research cohorts for numerous studies and clinical trials.

The Utah Population Database (UPDB) is one of the world’s most important collections of family history, demographic and medical data developed for scientific research. Built on a core of extensive Utah family history data from the LDS Church, UPDB integrates official state birth and death records, cancer diagnosis data and important medical and hospitalization records. The database is designed to allow the rapid addition of data from new sources, while preserving the integrity of all original data sources, which is critical for on-going database curation efforts. This database has been central to numerous important genetic and biomedical research projects at the University of Utah and elsewhere.

GenBank is the U.S. national repository for all known DNA sequences from all organisms. GenBank grew out of the Los Alamos DNA Sequence Library, originally created in the late 1970's, and the data collection effort continued at Los Alamos National Laboratory for the first ten years of the project. Michael Cinkosky played many roles in the project during that time, including taking the lead role in the design of the first version to use relational database technology, and the conversion from manual data entry to direct data submission from authors. This work enabled the GenBank project not only to keep up with exponentially increasing data (doubling every 18 months), but also to reduce the time required to incorporate new data from months to hours.

SIGMA is a tool for building genome maps that integrate data from many different experimental methods, such as genetic linkage mapping, physical clone mapping, and radiation hybrid mapping. This software was used to assemble maps of a number of human chromosomes early in the U.S. Human Genome Project, including the complete, integrated map of chromosome 16 published in Nature in 1995.

These laboratory information management systems (LIMS) are the central information systems for two University of Utah Core Facilities, handling all aspects of the work performed in these laboratories. These systems track each project from sample receipt to final delivery of analytical results.

This system was designed to reduce the administrative effort involved in using, running and supporting the shared, core facilities at the University of Utah. The system did not address the internals of any particular core facility, but rather it focused on automating many of the tasks common to all shared facilities, such as: order placement, progress tracking and billing. This greatly reduced the manual paperwork burden at each facility and provided a common interface to all their customers. In addition, it included a flexible programming interface so systems like the LIMS mentioned elsewhere could be integrated to produce a highly customized solution for individual core facilities.

Much of the research at the Huntsman Cancer Institute was focused on understanding the genetic factors involved in several types of cancer and success in this type of research often hinges on the identification, and tracking, of appropriate study cohorts. The systems listed here were all developed as part of this effort. Each system was built to support the protocols unique to a particular project, including initial screening, genetic counseling, genetic screening, tissue collection and follow-up exams. These projects included: High Risk Breast Cancer Clinic and the Familial Colon Cancer Clinic (now the Hereditary Gastrointestinal Cancer Registry). In the case of the Cancer Genetic Network system, selected data were then forwarded to the national CGN repository.

MutationDiscovery.com was a web resource for people using Transgenomic's WAVE system for genetic mutation discovery, detection and analysis. This site contained authoritative DNA sequences for over 100,000 genes from various organisms with details on over well over one million known genetic variations. This site also included PCR primer design and DHPLC amplicon melt profile analysis components. Due to changes in their business model, Transgenomic no longer actively maintains this site.

These administrative systems were designed to support the day-to-day operation of the Huntsman Cancer Institute, greatly streamlining many of the most labor-intensive aspects of this work. The Requisition and Purchasing system handled all of the tasks involved in the purchasing process within the Institute, including: generating a purchase requisition, requisition review and approval, order placement and fulfillment, and reconciliation with the university's central accounting system. The HR system was used to track essential information on all employees within the Institute.